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Structural Organisation Structural Organisation of Proteinsof Proteins

Dr. Mohammad AkramDr. Mohammad Akram

Metabolic LaboratoryMetabolic Laboratory

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ObjectivesObjectives

Purpose of the lecturePurpose of the lecture This session will describe what are This session will describe what are

proteins.proteins. Behavior of proteins in living organisms.Behavior of proteins in living organisms. Classification of protein functions.Classification of protein functions. At the conclusion of this session, you At the conclusion of this session, you

should understand the proteins and its should understand the proteins and its classification. classification.

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History of protein History of protein study study

The word The word PROTEINPROTEIN comes from Greek comes from Greek language (prota) which means "of language (prota) which means "of

primary importance". This name was primary importance". This name was introduced by Jons Jakob Berzelius in introduced by Jons Jakob Berzelius in

1838 for large organic compounds with 1838 for large organic compounds with almost equivalent empirical formulas. almost equivalent empirical formulas.

This name was used because the This name was used because the studied organic compounds were studied organic compounds were

primitive but seems to be very primitive but seems to be very important for nutrition. important for nutrition.

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Protein in living Protein in living organismsorganisms

Proteins are responsible for many Proteins are responsible for many different functions in the living cell. different functions in the living cell. It is possible to classify proteins on It is possible to classify proteins on

the basis of their functions. Very the basis of their functions. Very often, proteins can carry few often, proteins can carry few

functions and such proteins can be functions and such proteins can be placed into different groups, but placed into different groups, but

despite this, it is possible to assign despite this, it is possible to assign main group for each protein. main group for each protein.

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Protein Architecture

1. proteins are polymers consisting of amino acids linked by peptide bonds

2. each amino acid consists ofa central carbon atoman amino group NH2

a carboxylic group COOHa side chain

Difference in side chains distinguish different amino acids

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Amino acid: Basic unit Amino acid: Basic unit of proteinof protein

Different side chains, R, determine the properties of 20 amino acids.

COO-NH3+ C

R

H

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Peptide Bonds

Carboxyl groupSideChain

Aminogroup

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Each amino acid has Each amino acid has specific properties specific properties

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The Protein Folding

The function of a protein is determined by its 3D shape (fold, conformation)

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Type of structuresType of structures

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Type of StructureType of Structure

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Structural Levels of ProteinsStructural Levels of Proteins

Primary – linear sequence of amino acids composing the polypeptide chain (strand of amino acid “beads”)

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Structural Levels of Structural Levels of ProteinsProteins

SecondarySecondary – alpha – alpha helix or betahelix or beta pleated sheetspleated sheets

Both stabilized by Hydrogen bonds

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α-helixα-helix

A common feature in the A common feature in the secondary structuresecondary structure of of proteinsproteins, the , the alpha helix (α-helix)alpha helix (α-helix) is a right- or is a right- or left-handed coiled conformation, left-handed coiled conformation, resembling a resembling a springspring, in which every , in which every backbone backbone N-HN-H group donates a group donates a hydrogen bondhydrogen bond to the backbone to the backbone C=OC=O group of the group of the amino acidamino acid four four residues earlier ( hydrogen residues earlier ( hydrogen bonding). bonding).

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Beta helix Beta helix

A A beta helixbeta helix is a is a proteinprotein structure formed by the structure formed by the

association of parallel association of parallel beta strandsbeta strands in a helical pattern in a helical pattern with either two or three faces. with either two or three faces.

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Two-stranded helices Two-stranded helices

The simplest beta helix contains The simplest beta helix contains two "layers" of beta sheets two "layers" of beta sheets

connected by glycine-rich six-connected by glycine-rich six-residue loops that contain an residue loops that contain an

aspartate to bind one calcium ion aspartate to bind one calcium ion per loop. per loop.

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Structural Levels of Structural Levels of ProteinsProteinsTertiaryTertiary – superimposed folding of secondary – superimposed folding of secondaryStructures producing a ball-like or globular Structures producing a ball-like or globular

moleculemolecule

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Structural Levels of Structural Levels of ProteinsProteins

Quaternary – polypeptide chains Quaternary – polypeptide chains linked together in a specific linked together in a specific mannermanner

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Protein DenaturationProtein Denaturation

The activity of a protein depends on its three-dimensional structure.

Intramolecular bonds, especially hydrogen bonds, maintain the structure.

Hydrogen bonds may break when the pH drops or the temperature rises above normal

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Denaturisation processDenaturisation process

When protein unfolds and loses its three dimensional shape

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Protein FunctionsProtein Functions

1)1) Enzymatic catalysis. (e.g., enzymes)Enzymatic catalysis. (e.g., enzymes)

2)2) Transport and storage. (e.g., Hemoglobin & Transport and storage. (e.g., Hemoglobin & Myoglobin)Myoglobin)

3)3) Muscle motion. Muscle motion.

4)4) Mechanical support .Mechanical support .

5)5) Immune protection (e.g., Antibodies)Immune protection (e.g., Antibodies)

6)6) Generation and transmission of nerve impulses a Generation and transmission of nerve impulses a photoreceptor protein in retinal rod cell, which can photoreceptor protein in retinal rod cell, which can be triggered by acetylcholine, is responsible for be triggered by acetylcholine, is responsible for transmitting nerve impulses at synapses (i.e., at transmitting nerve impulses at synapses (i.e., at junctions between nerve cells)junctions between nerve cells)

7)7) Control of growth and differentiation (e.g., Nerve Control of growth and differentiation (e.g., Nerve growth factor)growth factor)

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SummarySummary

Proteins are key players in our living systems.Proteins are key players in our living systems. Proteins are polymers consisting of 20 kinds Proteins are polymers consisting of 20 kinds

of amino acids.of amino acids. Each protein folds into a unique three-Each protein folds into a unique three-

dimensional structure defined by its amino dimensional structure defined by its amino acid sequence.acid sequence.

Protein structure has a hierarchical nature.Protein structure has a hierarchical nature. Protein structure is closely related to its Protein structure is closely related to its

function.function. Protein structure prediction is a grand Protein structure prediction is a grand

challenge of computational biologychallenge of computational biology..

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THANK YOUTHANK YOU